def surfdist(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('surfdist',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('surfdist',self.vol_file,self.out_path,self.options)
self.text_dialog('Surface distance','Surface distance values for data from %s'%(self.vol_file),text,html)
def write_avgpd(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('average',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('average',self.vol_file,self.out_path,self.options)
self.text_dialog('Average packing','Average packing values for data from %s'%(self.vol_file),text,html)
def packing_report(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('report',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('report',self.vol_file,self.out_path,self.options)
self.text_dialog('Packing report','Packing report for %s'%(self.vol_file),text,html)
def write_cav(self,response=1):
if not self.vol_file:
self.select_first_message(".vol file")
return
self.get_options()
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
message = Voronoia.process_command('cavities',self.vol_dataset,self.vol_dataset,self.options)
else:
message = Voronoia.process_command('cavities',self.vol_file,self.out_path,self.options)
if response:
ms = Pmw.MessageDialog(self.parent,title="Cavities written as PDB file",message_text=message[0])
ms.activate()
ms.withdraw()
return message[1]
def compare_ref(self):
if not self.vol_file:
self.select_first_message(".vol file")
return
if not self.options['reference_file']:
self.select_first_message("reference file")
return
self.get_options()
self.options['reportmode']='both'
if self.vol_dataset:
self.options['dataset'] = self.vol_dataset
text,html = Voronoia.process_command('compare',self.vol_dataset,self.vol_dataset,self.options)
else:
text,html = Voronoia.process_command('compare',self.vol_file,self.out_path,self.options)
self.text_dialog('Packing compared to reference','Packing compared to reference values in\n%s'%(self.options['reference_file']),text,html)
def calc_packing(self,show_message=1):
# check for complete data
self.get_options()
if not self.input_file:
self.select_first_message("PDB file")
return
if not self.out_path:
self.select_first_message("output directory")
return
result = []
for in_file in self.get_vol_files():
# show calculation message
ms = Pmw.MessageDialog(title="Calculation running",buttons=[],message_text="""Packing data for the structure
%s
is being calculated. Please wait.
The calculation takes 1-15 minutes per file, depending on the size of the structure
and your hardware."""%in_file)
ms.show()
self.approot.update()
# calculate
message = Voronoia.process_command('calc',in_file,self.out_path,self.options)
result.append(message)
# destroy old message
ms.withdraw()
ms.destroy()
self.approot.update()
# set vol file variable
if self.pdb_dataset:
text = "%i packing files were calculated:\n"%len(result)
text += string.join(['\t'+name[1] for name in result],'\n')
if show_message:
ms = Pmw.MessageDialog(title=".vol files calculated",message_text=text)
self.vol_dataset = self.out_path
self.vol_file = result[0][1]
self.vol_file_var.set(self.vol_dataset)
self.vol_dataset_radio.setvalue(['Process all .vol files in this directory'])
return [name[1] for name in result]
else:
message = result[0]
if show_message:
ms = Pmw.MessageDialog(title=".vol file calculated",message_text=message[0])
self.vol_file = message[1]
self.vol_file_var.set(self._short_name(message[1]))
return message[1]
def __init__(self,app, pymol_gui=None):
# option settings
self.options = Voronoia.get_options()
self.options['atomtyping'] = 'few'
self.options['mode'] = 'packing_density'
# calculate tab elements
self.input_file = ""
self.input_file_var = StringVar()
self.input_file_var.set(self._short_name(self.input_file))
self.pdb_dataset = None
self.pdb_dataset_radio = None
self.out_path = os.getcwd()+os.sep
self.out_path_var = StringVar()
self.out_path_var.set(self.out_path)
self.exe_file_var = StringVar()
self.exe_file_var.set(self._short_name(self.options['executable']))
self.grid_dist_sel = None
# options tab elements
self.subset_radio = None
self.cavnb_radio = None
self.packing_mode_radio = None
self.atomtyping_radio = None
self.include_radio = None
self.radii_radio = None
# report tab elements
self.vol_file = ""
self.vol_file_var = StringVar()
self.vol_file_var.set(self._short_name(self.vol_file))
self.vol_dataset = None
self.vol_dataset_radio = None
self.ref_file_var = StringVar()
self.ref_file_var.set(self._short_name(self.options['reference_file']))
# now create the dialog
self.approot = app.root
dialog = Pmw.Dialog(self.approot,
buttons = ('About','Help', 'Quit'),
title = 'Voronoia Packing Toolbox',
command = self.execute)
dialog.withdraw()
parent = dialog.interior()
self.parent = parent
self.dialog = dialog
self.misc_text = None
self.misc_html = None
self.misc_dialog = None
# add logo
if PIL_FOUND:
self.voroidlogo = PhotoImage(file = "data"+os.sep+"voronoia.gif")
self.pymollogo = PhotoImage(file = "data"+os.sep+"pymol_logo.gif")
# ,bg='white'
can = Canvas(parent,height='96',width='280')
can.pack()
self.drawn = can.create_image(0,0,image=self.voroidlogo,anchor=NW)
# -------------- notebook tabs ----------------------
notebook = Pmw.NoteBook(parent)
notebook.pack(fill = 'both', expand = 1, padx = 0, pady = 0)
# ----- PyMOL stuff --------------------------------------
if pymol_gui:
pymol_gui.make_pymol_gui(self,notebook)
# ----- files --------------------------------------
page = notebook.add('Calculate Packing')
notebook.tab('Calculate Packing').focus_set()
# input file
frm = Frame(page)
frm.pack(fill='x',expand=1, padx = 10, pady = 2)
rb = Button(frm,text='Input PDB file',command=self.in_filedialog)
rb.pack(side=LEFT)
rl = Label(frm,textvariable=self.input_file_var,font=tkFont.Font(family="Helvetica",size="9",weight="normal"),relief='sunken', padx = 5, pady = 2)
rl.pack(side=LEFT,fill='x', expand=1, padx=10, pady=1)
# checkbox for dataset processing
frm = Frame(page)
frm.pack(fill='x',expand=0)
self.pdb_dataset_radio = Pmw.RadioSelect(frm,buttontype="checkbutton",orient='vertical')
self.pdb_dataset_radio.pack(side=LEFT,fill='both', expand=0, padx=10, pady=1)
self.pdb_dataset_radio.add('Process all PDB files in this directory',command=None)
# output path
frm = Frame(page)
frm.pack(fill='both',expand=1, padx = 10, pady = 2)
rb = Button(frm,text='Output directory',command=self.out_pathdialog)
rb.pack(side=LEFT)
rl = Label(frm,textvariable=self.out_path_var,justify=LEFT,wraplength=180,font=tkFont.Font(family="Helvetica",size="9",weight="normal"),relief='sunken', padx = 10, pady = 2)
rl.pack(side=LEFT,fill = 'x', expand = 1,padx=3)
# start calculation button
frm = Frame(page)
frm.pack(fill='both',expand=1, padx = 10, pady = 0)
button = Button(frm,text='Calculate packing file(s)',command=self.calc_packing)
button.pack(side=LEFT,fill='x',expand=1,pady=2)
# calculation parameters
group = Pmw.Group(page,tag_text='Calculation parameters')
group.pack(fill = 'both', expand = 1, padx = 0, pady = 0)
frm = Frame(group.interior())
frm.pack(fill='both',expand=1, padx = 0, pady = 0)
# grid distance selector
grid_dist = Pmw.OptionMenu(frm,
labelpos = 'w',label_text = 'Grid distance [Angstrom]',
items = ('0.20','0.10','0.05','0.02','0.01',),
)
grid_dist.pack(side=LEFT,fill='none',expand=0,padx=10)
self.grid_dist_sel = grid_dist
frm = Frame(group.interior())
frm.pack(fill='both',expand='1')
# radii set radiobuttons
radio = Pmw.RadioSelect(frm,buttontype="radiobutton",orient='vertical')
radio.pack(side=LEFT)
radio.add('ProtOr radii (Tsai 1999)')
radio.add('Stouten radii (Stouten 1993)')
radio.setvalue('ProtOr radii (Tsai 1999)')
self.radii_radio = radio
# hetero/water checkboxes
radio = Pmw.RadioSelect(frm,buttontype="checkbutton",orient='vertical')
radio.pack(side=RIGHT) # ,pady=3
radio.add('Include hetero groups',command=None)
radio.add('Include water molecules',command=None)
self.include_radio = radio
# change executable button
frm = Frame(group.interior())
frm.pack(fill='both',expand='1',padx=10)
rb = Button(frm,text='Change executable',command=self.exe_filedialog)
rb.pack(side=LEFT,fill='x',expand=0)
# --------------- Options ----------------
page = notebook.add('Options')
# buried / surface atoms
group = Pmw.Group(page,tag_text='Solvent acessibility')
group.pack(fill='both',expand=1, padx=4, pady=2)
frm = Frame(group.interior())
frm.pack(fill='both',expand='1')
radio = Pmw.RadioSelect(frm,buttontype="checkbutton",orient='vertical')
radio.pack(side=LEFT)
radio.add('include buried atoms',command=None)
radio.add('include solvent accessible atoms',command=None)
radio.setvalue(['include buried atoms'])
self.subset_radio = radio
# cavity-neighbor / non-neighbor atoms
group = Pmw.Group(page,tag_text='Cavity neighbors')
group.pack(fill='both',expand=1, padx=4, pady=2)
frm = Frame(group.interior())
frm.pack(fill='both',expand='1')
radio = Pmw.RadioSelect(frm,buttontype="checkbutton",orient='vertical')
radio.pack(side=LEFT)
radio.add('include cavity neighbor atoms',command=None)
radio.add('include all other atoms',command=None)
radio.setvalue(['include cavity neighbor atoms','include all other atoms'])
self.cavnb_radio = radio
# write packing densities or volumes
group = Pmw.Group(page,tag_text='Output data type')
group.pack(side=TOP,fill='both',expand=1, padx=4, pady=2)
radio = Pmw.RadioSelect(group.interior(),buttontype="radiobutton",orient='vertical')
radio.pack(side=LEFT)
radio.add('atomic packing densities')
radio.add('atomic volumes')
radio.setvalue('atomic packing densities')
self.packing_mode_radio = radio
# concise or long atom types
group = Pmw.Group(page,tag_text='Atom typing')
group.pack(side=TOP,fill='both',expand=1, padx=4, pady=2)
radio = Pmw.RadioSelect(group.interior(),buttontype="radiobutton",orient='vertical')
radio.pack(side=LEFT)
radio.add('19 ProtOr atom types')
radio.add('173 explicit atom types')
radio.setvalue('19 ProtOr atom types')
self.atomtyping_radio = radio
# surfdist parameters
group = Pmw.Group(page,tag_text='Surface distance parameters')
group.pack(fill = 'both', expand = 1, padx = 0, pady = 0)
frm = Frame(group.interior())
frm.pack(fill='both',expand=1, padx = 0, pady = 0)
n_bins = Pmw.OptionMenu(frm,
labelpos = 'w',label_text = 'number of bins',
items = ('10','20','50','100',),
initialitem='20'
)
max_depth = Pmw.OptionMenu(frm,
labelpos = 'w',label_text = 'maximum depth [Angstrom]',
items = ('5.0','10.0','15.0','20.0'),
initialitem='10.0'
)
n_bins.pack(side=LEFT,fill='none',expand=0,padx=10)
max_depth.pack(side=LEFT,fill='none',expand=0,padx=10)
self.n_bins_sel = n_bins
self.maxdepth_sel = max_depth
# Pmw.Color.changecolor(page, background = 'white',foreground='#000070')
# ------------- actions -----------------
page = notebook.add('Results')
# input .vol file(s)
group = Pmw.Group(page,tag_text='Packing files')
group.pack(fill = 'x', expand = 1, padx = 10, pady = 2)
frm = Frame(group.interior())
frm.pack(fill='x',expand=1, padx = 10, pady = 2)
rb = Button(frm,text='Choose .vol file',command=self.vol_filedialog)
rb.pack(side=LEFT)
rl = Label(frm,textvariable=self.vol_file_var,font=tkFont.Font(family="Helvetica",size="9",weight="normal"),relief='sunken', padx = 5, pady = 2)
rl.pack(side=LEFT,fill='x', expand=1, padx=10, pady=1)
# checkbox for dataset processing
frm = Frame(group.interior())
frm.pack(fill='x',expand=0)
self.vol_dataset_radio = Pmw.RadioSelect(frm,buttontype="checkbutton",orient='vertical')
self.vol_dataset_radio.pack(side=LEFT,fill='both', expand=0, padx=10, pady=1)
self.vol_dataset_radio.add('Process all .vol files in this directory',command=None)
# Reports
group = Pmw.Group(page,tag_text='Report')
group.pack(fill = 'x', expand = 1, padx = 10, pady = 2)
rb = Button(group.interior(),text='Create packing report',command=self.packing_report)
rb.pack(fill='x',expand=1, padx = 10, pady = 2)
rb = Button(group.interior(),text='Calculate average packing',command=self.write_avgpd)
rb.pack(fill='x',expand=1, padx = 10, pady = 2)
# compare to reference values
group = Pmw.Group(page,tag_text='Reference data')
group.pack(fill = 'x', expand = 1, padx = 10, pady = 2)
frm = Frame(group.interior())
frm.pack(fill='x',expand=1, padx = 10, pady = 2)
rb = Button(frm,text='Choose reference file',command=self.ref_filedialog)
rb.pack(side=LEFT)
rl = Label(frm,textvariable=self.ref_file_var,font=tkFont.Font(family="Helvetica",size="9",weight="normal"),relief='sunken', padx = 5, pady = 2)
rl.pack(side=LEFT,fill='x', expand=1, padx=10, pady=1)
rb = Button(group.interior(),text='Compare .vol file to reference data',command=self.compare_ref)
rb.pack(fill='x',expand=1, padx = 10, pady = 2)
# report surface distances
group = Pmw.Group(page,tag_text='Surface distance statistics')
group.pack(fill = 'x', expand = 1, padx = 10, pady = 2)
rb = Button(group.interior(),text='Report distance to surface',command=self.surfdist)
rb.pack(fill='x',expand=1, padx = 10, pady = 2)
# write cavity coordinates
group = Pmw.Group(page,tag_text='PDB output')
group.pack(fill = 'x', expand = 1, padx = 10, pady = 2)
rb = Button(group.interior(),text='Write cavities as PDB',command=self.write_cav)
rb.pack(fill='x',expand=1, padx = 10, pady = 2)
rb = Button(group.interior(),text='Write cavity neighbors as PDB',command=self.write_cavnb)
rb.pack(fill='x',expand=1, padx = 10, pady = 2)
# Pmw.Color.changecolor(page, background = 'white',foreground='#000070')
notebook.recolorborders()
notebook.setnaturalsize()
dialog.show()
